You have to mark the script as an executable after creating it, using:

$ chmod +x run.sh

Create a plot

Run the script after loading the CP2K module:

$ ./run.sh

Besides various input and output files, you should get a file named energies.

Plot it, including meaningful axis labels. To that end, try to understand the provided script. Looking at the difference between the initially provided input file h2o_pbc.inp and the newly created input files may give a hint. The command $ diff h2o_pbc.inp SOMEOTHERFILE may also help.

What would you expect from such a plot and why? What order is the deviation from what you would expect? What could be the source for this deviation?

Make the script your own

Read the script and try to understand the commands. Look them up using your favorite search engine, the man pages on the system ($ man sed for example) or try them out by hand on the command line.

Try to document the script in such a way that you will still understand it when looking at it again in a year or two (so, not every detail, but make sure to cover the obscure stuff and the big blocks)

Change the script to calculate energies for x=z=5. and y=2,2.2,2.4,..,7.6,7.8,8.0 and plot them again.